Introduction: Prion diseases are unique fatal neurodgenerative diseases caused by novel pathogens termed prions. The major or only component of prions is an abnormal form of a normal cellular protein termed the prion protein (PrP). The normal form (PrPC) is converted to the pathogenic form (PrPSc) by an as yet unidentified posttranslational process. Mass spectrometry is essential for the detailed analysis of small-scale samples of both forms of the prion protein isolated from the brains of hamsters. Methods: Several novel methods have been refined for the analysis of PrPSc using LSIMS, ESIMS, MALDI and MS/MS for the characterization of peptides and oligosaccharides from enzyme digests. These analyses are complicated by the hydrophobic, insoluble and strongly aggregating propoerties, particularly of PrPSc. PrPC analyses have been delayed by problems of purifying the protein from brain. Preliminary results by MALDI show that the two forms are similar, but microheterogeneity has prevented any definitive conclusions being drawn. Comparisons are also required between PrPSc from different prion strains. Strain behavior could be due to differences in the N-linked oligosaccharides; perhaps cell specific lectins cause targetting of certain PrP species to a limited range of cell types, resulting in regional distribution of PrPSc. We plan to use LC/MS for much of this characterization. Discussion: Results obtained so far suggest that the modification of PrPC involved in the formation of PrPSc may be conformational rather than chemical. It is essential to confirm that PrpC and PrPSc either are or are not identical in order to develop hypotheses for the molecular mechanisms of prion diseases.